TUTORIAL
PURPOSE
· Help you appreciate the diversity of organs.
· Help you comprehend the types of information associated with an organ.
·
Develop a template for structuring this
multi-dimensional information, so that you can use this template for organizing
the information associated with the large variety of organs.
PRE-CLASS OBJECTIVES
· Develop a provisional definition of ‘organ’ based on intuitive criteria you use for assigning a set of anatomical structures to this class.
· Refine your provisional definition based on the definition of ‘organ’ in dictionaries and the FM.
· Based on your exploration of textbook chapters and anatomical images, as well as your categorization of anatomical information, propose a set of descriptors (attributes) that capture the knowledge associated with an organ.
PREPARATION FOR CLASS
1. Update your knowledge
Revisit the “Recapitulation” sections of the tutorial for the previous class and update/enhance the documents you generated based on what you have learned in class.
In particular, update the term list you generated in the previous tutorial with respect to
·
classification of the entities
represented by the terms (anatomical structure, body substance, etc);
·
anatomical relationship ontology in terms
of Ao, ASA and ATA relationships.
Know how to
locate terms in the Ao of FM, FM definitions, and the ontology of ASA
relationships.
2.
Develop
a provisional definition of ‘organ’ based on intuitive criteria you use for
assigning a set of anatomical structures to this class.
Make a new copy of your term list and write ‘organ’ beside those that you intuitively consider as organs.
If less than a dozen terms meet your criteria, add some anatomical structures that you would classify as organs, and designate them as such.
Perform the same exercise with respect to structures that are smaller than organs and you consider them to be parts of organs. Label them ‘organ part’. Try to generate at least a dozen such terms.
Do the same for the structures that are larger/more complex than organs (e.g. head, trunk, or GI tract) and label them ‘body part’ or organ system’, if you can make this distinction, or if not, label them ‘larger than organ’. Try to generate at least a dozen such terms.
Are there any reaming anatomical structures in the list that are unclassified? Invent a class for them (‘other’ will do).
Re-sort your list of anatomical structures to show children of ‘organ’, ‘organ part’, ‘larger than organ’ (or ‘body part’, ‘organ system’), and save it as ‘Organ ontology, Version 1’.
Think about the criteria you used for deciding whether an anatomical structure was an organ or not.
Make a list of these criteria and save it as “My defining criteria (attributes) for organ; Version 1”.
Based on these criteria, write your own definition of ‘organ’ and save it as version 1.
3.
Refine
your provisional definition based on the definition of ‘organ’ in dictionaries
and the FM.
We hope you were able to resist reading the definitions in the ‘resource’ for the class, until you have formulated your own.
Now access the definitions we provided for you and any other definition of ‘organ’ you care to track down. If you find new and alternative definitions, please share them with us.
Resource:
Evaluate these definitions critically.
Make a list of the defining criteria that are embedded in them and save the list as ‘Official defining criteria for organ’.
Compare these ‘official defining’ criteria with your own criteria.
Before amending your own criteria and definition, evaluate the ‘official’ as well as your own definitions by the following exercise.
Before we suggest an approach, give some thought to how you would go about checking whether these definitions are valid or whether they have holes in them.
This is not an easy task, but write down the methods/approaches you can propose for validating definitions.
Save the document as ‘Definition validation’.
Apply the approach you suggest to definitions of organ.
Once you have applied your approach, compare it two-pronged approach suggested below:
a.) test whether structures that are universally accepted as organs satisfy the defining criteria embedded in the definition;
b.) test whether the defining criteria embedded in the definition exclude those structures that would definitely not be regarded as organs.
However poorly defined their criteria are, every one would agree that heart, lung and kidney are organs (think of the term ‘organ donor’), whereas no one would regard the right atrium, lobe of lung, the hand and the head, or a red blood cell and sperm as organs.
Using some, or all of these examples, reason your way through the official definitions of organ, as well as your own definition.
Do the exercise in writing (see below).
As part of this process you will have to be clear about the definitions of other anatomical structures that are included in these definitions (e.g., tissue). Find such definitions from the course resources or on your own initiative.
The example below uses the ‘hand’ to illustrate how you should perform the exercise when you are evaluating the second Dorland definition. For each criterion in the definition ask yourself the question, ‘true?’.
“a somewhat independent part of the body
true for hand
that is arranged according to a characteristic structural plan,
true; hand has a characteristic structural
plan: 5 digits, fixed number of bones in each, etc.
and performs a special function or functions;
true; grasping, gathering tactile information
it is composed of various tissues, one of which is primary in function.”
more or less true (you need to know what
tissues are);
hand is composed of various tissues (muscle
tissue, bone tissue, epithelium in the skin, neural tissue in nerves,
connective tissue in tendons and fat);
muscle may be considered primary tissue in
grasping function and epithelium and nervous tissue in tactile functions.
Conclusion:
1. hand satisfies defining criteria for organ in this definition;
2. hand must either be an organ or the defining criteria for organ in the definition are invalid.
Is the Dorland definition too broad or too narrow for organ?
We are particularly interested in you finding inconsistencies and problems in the FM definition. Please give us feedback.
This exercise should illustrate to you how difficult it is to write logically sound, explicit and specific definitions.
Rewrite your defining criteria for organ and rewrite your definition based on what you have learned form the exercise. Save them as versions 2.
4.
Based
on your exploration of textbook chapters and anatomical images, as well as your
categorization of anatomical information, propose a set of descriptors
(attributes) that capture the knowledge associated with an organ.
In the last tutorial and class you classified the kinds of anatomical information associated with various anatomical entities.
In class we extended this list in terms of the ASA and ATA components of the Foundational Model.
Your task now is to select from these sources the kinds of information (or relationships) that are necessary to capture knowledge about an organ.
In other words, what would you like to know about an organ? Any organ
These questions are not directly retrievable from sources of anatomical information, but surveying some of the sources will give you ideas about the kinds of knowledge that characterize an organ.
In the next class, we will use the lung as a specific example of a particular class of organ and will gather the information specifically relevant to it.
However, in order to generate the questions that should be included in the ‘knowledge organization template’ (KOT) of any organ, you should survey a few on-line anatomy programs.
Course resources direct you to a number of URLs.
Some of these are organized as atlases, others as electronic texts, yet others are image data without any annotations.
Select 3-4 organs from your own list of organs and explore a few of the web-based anatomy programs to assess whether
· they deal with your selected organs;
· what kind of information they present about an organ of your interest.
Based on this experience, write down a set of questions that need to be answered in order to capture the anatomical knowledge necessary to characterize an organ.
Your questions will provide the basis for developing a KOT for organ in class.
The answers to these questions will represent the attributes that characterize an organ.
REQUEST
Share the documents you generated with members of the class and your instructors.
PROBLEM TO THINK ABOUT
1. Organ Harvest Game.
How would you develop an interactive game that teaches organ classification using terms or images?
The purpose of the ‘Organ Harvest’ game is to
· prompt the learner to consider the criteria by which a structure is classified as an organ;
· reinforce what was learned in Tutorial 1 about the kinds of objects that constitute the body;
· evaluate knowledge about characteristics of organs.
2. Template Maker
How could develop a tool, which relying on knowledge represented in the FM, could specify the fields of knowledge organization templates for different kinds of anatomical entities?